You would use the office your stay is registered with.
With regard to your visa 90, which visa is it? there are many and many people call them misleading short names. And they have different steps forward to a 12 month extension.
If you'd be prepared to deposit ฿800k into a Thai bank you could get a non-o retirement here if over 50 years old, and not have to leave each year when you extend again. Alternatively there's many a visa agent that can help for a fee.
I'd get to the Thai mainland, then take the train or minivan south to Hat Yai, cross the border on the train at Padang Besar and take the train south through Malaysia.
I used Chiang Wattana IO in Bangkok. Yes it's huge, but it was very efficient and well organised. I was normally seen within minutes of my appointment time and out in less than an hour. No agent needed, it would probably take a similar amount of time and effort but be paying much more.